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[bioontology-support] search by id in a subtree

John Graybeal jgraybeal at
Wed Feb 14 15:11:02 PST 2018

I'm going to try to get this right, but I may need help from the professionals.

To my knowledge, BioPortal does not parse mappings that are contained within ontologies, so a linkage would not appear in that way. However, BioPortal does watch for the same IRI appearing in multiple ontologies, and will indicate the relationship between those two entities. (I don't *think* it uses the sameAs or exactMatch relations at that point either.)

It is possible to map any two classes that are within BioPortal ontologies. The most documentation we have on this was captured in a thread just yesterday; read to the last post of for this information.

There is an issue in the AgroPortal github issues about adding the ability to the AgroPortal to parse mappings contained in ontologies ( We stay in close communication with AgroPortal, and if that goes forward, we would be hoping to use the same approach. Unfortunately their handling of mappings is more general than BioPortal's right now, so it might not be an easy port. (Read: Don't hold your breath for BioPortal to have it soon.)


From: bioontology-support <bioontology-support-bounces at> on behalf of Madani, Sina <Sina.Madani at>
Sent: Wednesday, February 14, 2018 11:33 AM
To: Michael Dorf; support at
Subject: Re: [bioontology-support] search by id in a subtree


I have another question while support is working on my previous one ☺

If I provide a linkage between two classes from two ontologies through skos:exactMatch (or other mapping types) in my TTL file, does such linkage appear (under mapping) in Ontoportal when I load the ttl as an ontology submission in our local appliance instance ? is it possible to map two classes within the same ontology?


From: Michael Dorf <mdorf at>
Date: Wednesday, January 31, 2018 at 6:05 PM
To: "support at" <support at>
Cc: "Madani, Sina" <Sina.Madani at>
Subject: Fwd: [bioontology-support] search by id in a subtree


I am using a local version of Appliance 2.5 RC3 as well as UMLS2RDF script against UMLS2017AB database to generate and load SNOMED.ttl file (1.29Gb).

However, upon submitting a new ontology and after few seconds I get this error message in the web UI: “something went wrong”. Also, http://ontotoportal.admin<> report under issues section shows “ontology has no submission”.  Under /srv/ncbo/repository path no directory was created for SNOMED. Seems manually creating “1” submission directory and copying SNOMED ttl into that directory doesn’t have any effect even with manual parsing per instruction. Is it possible to manually load large ttl files and create submissions?

Scheduler.log or appliance.log doesn’t show any error either.

I re-tried the submission with a compressed tar file (72 Mb) too. This time,  http://ontotoportal.admin<> showed ERROR_RDF under Error Status field. Also, on admin page, the log link under URL field shows below messages.  It seems manually unzipping the file and/or reprocessing it doesn’t have any effect either

Is there a workaround for loading/parsing SNOMED (or similar large ontologies) into OntoPortal? Also, is it possible to access 4store directly in our local instance from a sparql endpoint similar to Bioportal website?



I, [2018-01-28T11:19:17.181176 #3910]  INFO -- : ["Starting to process"<>]

I, [2018-01-28T11:19:17.219473 #3910]  INFO -- : ["Starting to process SNOMED/submissions/1"]

I, [2018-01-28T11:19:17.338663 #3910]  INFO -- : ["Using UMLS turtle file found, skipping OWLAPI parse"]

E, [2018-01-28T11:19:17.338923 #3910] ERROR -- : ["ArgumentError: invalid byte sequence in UTF-8\n/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:398:in `block in generate_umls_metrics_file'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:397:in `foreach'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:397:in `generate_umls_metrics_file'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:414:in `generate_rdf'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/bundler/gems/ontologies_linked_data-ff5920539091/lib/ontologies_linked_data/models/ontology_submission.rb:903:in `process_submission'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:177:in `process_submission'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:47:in `block in process_queue_submissions'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:41:in `each'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/ontology_submission_parser.rb:41:in `process_queue_submissions'\n\t/srv/ncbo/ncbo_cron/bin/ncbo_cron:228:in `block (3 levels) in <main>'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:65:in `block (3 levels) in scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:51:in `fork'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:51:in `block (2 levels) in scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/mlanett-redis-lock-0.2.7/lib/redis-lock.rb:43:in `lock'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/mlanett-redis-lock-0.2.7/lib/redis-lock.rb:234:in `lock'\n\t/srv/ncbo/ncbo_cron/lib/ncbo_cron/scheduler.rb:50:in `block in scheduled_locking_job'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/jobs.rb:230:in `trigger_block'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/jobs.rb:204:in `block in trigger'\n\t/srv/ncbo/ncbo_cron/vendor/bundle/ruby/2.3.0/gems/rufus-scheduler-2.0.24/lib/rufus/sc/scheduler.rb:430:in `block in trigger_job'"]

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